diff commons/launcher/tests/Test_BlatProgramLauncher.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/tests/Test_BlatProgramLauncher.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,98 @@
+import unittest
+from commons.launcher.BlatProgramLauncher import BlatProgramLauncher
+
+
+class Test_BlatProgramLauncher( unittest.TestCase ):
+    
+    def setUp( self ):
+        self._i = BlatProgramLauncher()
+        
+        
+    def tearDown( self ):
+        self._i = None
+        
+        
+    def test_getHelpAsString( self ):
+        exp = ""
+        exp += "usage: BlatProgramLauncher.py [options]" 
+        exp += "\ngeneric options:"
+        exp += "\n     -h: this help"
+        exp += "\n     -i: name of the input file (format='fasta')"
+        exp += "\n     -c: clean"
+        exp += "\n     -v: verbosity level (default=0/1)"
+        exp += "\nspecific options:"
+        exp += "\n     -s: name of the subject file (database, format='fasta')"
+        exp += "\n     -p: parameters for 'blat'"
+        exp += "\n     -A: same sequences (all-by-all)"
+        exp += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
+        obs = self._i.getHelpAsString()
+        self.assertEqual( exp, obs )
+        
+        
+    def test_setAttributesFromCmdLine( self ):
+        self._i.setAttributesFromCmdLine( "-s", "dummySubjectFile.fa" )
+        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
+        
+        self._i.setAttributesFromCmdLine( "-o", "dummyOutFile.align" )
+        self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
+        
+        
+    def test_setWrapperCommandLine( self ):
+        self._i.setInputFile( "dummyInFile.fa" )
+        self._i.setSubjectFile( "dummySubjectFile.fa" )
+        exp = "BlatProgramLauncher.py"
+        exp += " -i %s" % ( "dummyInFile.fa" )
+        exp += " -s %s" % ( "dummySubjectFile.fa" )
+        exp += " -o %s.align" % ( "dummyInFile.fa" )
+        exp += " -v 0"
+        self._i.setWrapperCommandLine()
+        obs = self._i.getWrapperCommandLine()
+        self.assertEqual( exp, obs )
+        
+        
+    def test_setProgramCommandLine( self ):
+        self._i.setInputFile( "dummyInFile.fa" )
+        self._i.setSubjectFile( "dummySubjectFile.fa" )
+        self._i.setProgramParameters( "-minIdentity=90" )
+        exp = "blat dummySubjectFile.fa dummyInFile.fa -minIdentity=90 -out=blast8 dummyInFile.fa.blast"
+        self._i.setProgramCommandLine()
+        obs = self._i.getProgramCommandLine()
+        self.assertEqual( exp, obs )
+        
+        
+    def test_setListFilesToKeep( self ):
+        self._i.setInputFile( "dummyInFile.fa" )
+        lExp = [ "dummyInFile.fa.align" ]
+        self._i.setListFilesToKeep()
+        lObs = self._i.getListFilesToKeep()
+        lExp.sort()
+        lObs.sort()
+        self.assertEqual( lExp, lObs )
+        
+        
+    def test_setListFilesToRemove( self ):
+        self._i.setInputFile( "dummyInFile.fa" )
+        lExp = [ "dummyInFile.fa.blast" ]
+        self._i.setListFilesToRemove()
+        lObs = self._i.getListFilesToRemove()
+        lExp.sort()
+        lObs.sort()
+        self.assertEqual( lExp, lObs )
+        
+        
+    def test_setSummary( self ):
+        self._i.setInputFile( "dummyInFile.fa" )
+        self._i.setSubjectFile( "dummySubjectFile.fa" )
+        exp = "input file: %s" % ( self._i.getInputFile() )
+        exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
+        exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
+        exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
+        self._i.setSummary()
+        obs = self._i.getSummary()
+        self.assertEqual( exp, obs )
+        
+        
+test_suite = unittest.TestSuite()
+test_suite.addTest( unittest.makeSuite( Test_BlatProgramLauncher ) )
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run( test_suite )